Molecular cytogenetic characterization of repetitive sequences comprising centromeric heterochromatin in three Anseriformes species

Abstract

The highly repetitive DNA sequence of centromeric heterochromatin is an effective molecular cytogenetic marker for investigating genomic compartmentalization between macrochromosomes and microchromosomes in birds. We isolated four repetitive sequence families of centromeric heterochromatin from three Anseriformes species, viz., domestic duck (Anas platyrhynchos, APL), bean goose (Anser fabalis, AFA), and whooper swan (Cygnus cygnus, CCY), and characterized the sequences by molecular cytogenetic approach. The 190-bp APL-HaeIII and 101-bp AFA-HinfI-S sequences were localized in almost all chromosomes of A. platyrhynchos and A. fabalis, respectively. However, the 192-bp AFA-HinfI-L and 290-bp CCY-ApaI sequences were distributed in almost all microchromosomes of A. fabalis and in approximately 10 microchromosomes of C. cygnus, respectively. APL-HaeIII, AFA-HinfI-L, and CCY-ApaI showed partial sequence homology with the chicken nuclear-membrane-associated (CNM) repeat families, which were localized primarily to the centromeric regions of microchromosomes in Galliformes, suggesting that ancestral sequences of the CNM repeat families are observed in the common ancestors of Anseriformes and Galliformes. These results collectively provide the possibility that homogenization of centromeric heterochromatin occurred between microchromosomes in Anseriformes and Galliformes; however, homogenization between macrochromosomes and microchromosomes also occurred in some centromeric repetitive sequences.

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

“…3a and b , green arrowheads). Consistent with the reported karyotypes of duck and other birds [ 50 , 51 ], almost all microchromosomes are acrocentric, indicated by their positions in the centromeric region. Both macro- and microchromosomes' centromeres are enriched for CR1-J2_Pass repeats ( Supplementary Fig.…”

“…The completeness of our new duck genome is also demonstrated by its assembled centromeres (mean length 443.3 kb) and telomeres (mean length 73.7 kb), which were annotated by a cytogenetically verified Anseriformes centromeric repeat (APL-HaeIII) [ 50 ] and conserved telomeric motif sequences ( Supplementary Table S4 and S5 ). We found 22 telomeric sites among the 31 chromosomes, of which 11 were interstitial telomeric repeat (ITR) sites inside the chromosomes (Fig.…”

“…To annotate the putative centromeres, we searched the genome with the reported 190-bp duck centromeric repeats [ 50 ] using TRFinder [ 106 ] (v4.09) with the following parameters: 2 5 7 80 10 50 2000. A genome-wide distribution of the 190-bp sequences was generated by binning the genome with a 50-kb non-overlapping window to find the local enrichment of copy numbers, which was defined as the putative centromeres.…”

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

“…In addition, all chromosomes but chrZ(Figure 3a)show generally equal expression levels between sexes; genes on chrZ are expressed twice the level in males versus females. These chromosome-wide patterns are consistent with those reported in other birds regarding the differences between micro-and macrochromosomes, and a lack of global dosage compensation on avian sex chromosomes[1,48,49].The completeness of our new duck genome is also demonstrated by its assembled centromeres (average length 443.3 kb) and telomeres (average length 73.7 kb), which were annotated by a cytogenetically verified Anseriformes centromeric repeat (APL-HaeIII)[50] and conserved telomeric motif sequences (Supplementary Table S4-5). We found 22 telomeric sites among the 31 chromosomes, of which 11 were interstitial telomeric repeat (ITR) sites inside the chromosomes(Figure 3a-b, green arrow heads).…”

“…To annotate the putative centromeres, we searched the genome with the reported 190bp duck centromeric repeats [50] using TRFinder [105] (v4.09) with the parameters: 2 5 7 80 10 50 2000. A genome-wide distribution of the 190bp sequences was generated by binning the genome with a 50kb non-overlapping window to find the local enrichment of copy numbers, which was defined as the putative centromeres.…”